/********************************************************************** * cbf_compress -- compression and decompression * * * * Version 0.8.0 20 July 2008 * * * * Paul Ellis and * * Herbert J. Bernstein (yaya@bernstein-plus-sons.com) * * * * (C) Copyright 2006, 2007 Herbert J. Bernstein * * * **********************************************************************/ /********************************************************************** * * * YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL * * * * ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS * * OF THE LGPL * * * **********************************************************************/ /*************************** GPL NOTICES ****************************** * * * This program is free software; you can redistribute it and/or * * modify it under the terms of the GNU General Public License as * * published by the Free Software Foundation; either version 2 of * * (the License, or (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program; if not, write to the Free Software * * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA * * 02111-1307 USA * * * **********************************************************************/ /************************* LGPL NOTICES ******************************* * * * This library is free software; you can redistribute it and/or * * modify it under the terms of the GNU Lesser General Public * * License as published by the Free Software Foundation; either * * version 2.1 of the License, or (at your option) any later version. * * * * This library is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * * Lesser General Public License for more details. * * * * You should have received a copy of the GNU Lesser General Public * * License along with this library; if not, write to the Free * * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, * * MA 02110-1301 USA * * * **********************************************************************/ /********************************************************************** * * * Stanford University Notices * * for the CBFlib software package that incorporates SLAC software * * on which copyright is disclaimed * * * * This software * * ------------- * * The term Ôthis softwareÕ, as used in these Notices, refers to * * those portions of the software package CBFlib that were created by * * employees of the Stanford Linear Accelerator Center, Stanford * * University. * * * * Stanford disclaimer of copyright * * -------------------------------- * * Stanford University, owner of the copyright, hereby disclaims its * * copyright and all other rights in this software. Hence, anyone * * may freely use it for any purpose without restriction. * * * * Acknowledgement of sponsorship * * ------------------------------ * * This software was produced by the Stanford Linear Accelerator * * Center, Stanford University, under Contract DE-AC03-76SFO0515 with * * the Department of Energy. * * * * Government disclaimer of liability * * ---------------------------------- * * Neither the United States nor the United States Department of * * Energy, nor any of their employees, makes any warranty, express or * * implied, or assumes any legal liability or responsibility for the * * accuracy, completeness, or usefulness of any data, apparatus, * * product, or process disclosed, or represents that its use would * * not infringe privately owned rights. * * * * Stanford disclaimer of liability * * -------------------------------- * * Stanford University makes no representations or warranties, * * express or implied, nor assumes any liability for the use of this * * software. * * * * Maintenance of notices * * ---------------------- * * In the interest of clarity regarding the origin and status of this * * software, this and all the preceding Stanford University notices * * are to remain affixed to any copy or derivative of this software * * made or distributed by the recipient and are to be affixed to any * * copy of software made or distributed by the recipient that * * contains a copy or derivative of this software. * * * * Based on SLAC Software Notices, Set 4 * * OTT.002a, 2004 FEB 03 * **********************************************************************/ /********************************************************************** * NOTICE * * Creative endeavors depend on the lively exchange of ideas. There * * are laws and customs which establish rights and responsibilities * * for authors and the users of what authors create. This notice * * is not intended to prevent you from using the software and * * documents in this package, but to ensure that there are no * * misunderstandings about terms and conditions of such use. * * * * Please read the following notice carefully. If you do not * * understand any portion of this notice, please seek appropriate * * professional legal advice before making use of the software and * * documents included in this software package. 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CIF (Hall, Allen & Brown, 1991) is the * * recommended method for submitting publications to Acta * * Crystallographica Section C and reports of crystal structure * * determinations to other sections of Acta Crystallographica * * and many other journals. The syntax of a CIF is a subset of the * * more general STAR File[2] format. The CIF and STAR File approaches * * are used increasingly in the structural sciences for data exchange * * and archiving, and are having a significant influence on these * * activities in other fields. * * * * Statement of intent * * * * The IUCr's interest in the STAR File is as a general data * * interchange standard for science, and its interest in the CIF, * * a conformant derivative of the STAR File, is as a concise data * * exchange and archival standard for crystallography and structural * * science. * * * * Protection of the standards * * * * To protect the STAR File and the CIF as standards for * * interchanging and archiving electronic data, the IUCr, on behalf * * of the scientific community, * * * * * holds the copyrights on the standards themselves, * * * * * owns the associated trademarks and service marks, and * * * * * holds a patent on the STAR File. * * * * These intellectual property rights relate solely to the * * interchange formats, not to the data contained therein, nor to * * the software used in the generation, access or manipulation of * * the data. * * * * Promotion of the standards * * * * The sole requirement that the IUCr, in its protective role, * * imposes on software purporting to process STAR File or CIF data * * is that the following conditions be met prior to sale or * * distribution. * * * * * Software claiming to read files written to either the STAR * * File or the CIF standard must be able to extract the pertinent * * data from a file conformant to the STAR File syntax, or the CIF * * syntax, respectively. * * * * * Software claiming to write files in either the STAR File, or * * the CIF, standard must produce files that are conformant to the * * STAR File syntax, or the CIF syntax, respectively. * * * * * Software claiming to read definitions from a specific data * * dictionary approved by the IUCr must be able to extract any * * pertinent definition which is conformant to the dictionary * * definition language (DDL)[3] associated with that dictionary. * * * * The IUCr, through its Committee on CIF Standards, will assist * * any developer to verify that software meets these conformance * * conditions. * * * * Glossary of terms * * * * [1] CIF: is a data file conformant to the file syntax defined * * at http://www.iucr.org/iucr-top/cif/spec/index.html * * * * [2] STAR File: is a data file conformant to the file syntax * * defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html * * * * [3] DDL: is a language used in a data dictionary to define data * * items in terms of "attributes". Dictionaries currently approved * * by the IUCr, and the DDL versions used to construct these * * dictionaries, are listed at * * http://www.iucr.org/iucr-top/cif/spec/ddl/index.html * * * * Last modified: 30 September 2000 * * * * IUCr Policy Copyright (C) 2000 International Union of * * Crystallography * **********************************************************************/ #ifdef __cplusplus extern "C" { #endif #include #include #include #include #include "cbf.h" #include "cbf_alloc.h" #include "cbf_file.h" #include "cbf_compress.h" #include "cbf_canonical.h" #include "cbf_packed.h" #include "cbf_byte_offset.h" #include "cbf_nibble_offset.h" #include "cbf_predictor.h" #include "cbf_uncompressed.h" /* Compress an array */ int cbf_compress (void *source, size_t elsize, int elsign, size_t nelem, unsigned int compression, cbf_file *file, size_t *compressedsize, int *bits, char *digest, int realarray, const char *byteorder, size_t dimfast, size_t dimmid, size_t dimslow, size_t padding) { int errorcode; size_t size; const char * compression_name; /* Discard any bits in the buffers */ cbf_failnez (cbf_reset_bits (file)) if (compressedsize) *compressedsize = 0; /* Start a digest? */ if (digest) cbf_failnez (cbf_start_digest (file)) errorcode = 0; size = 0; compression_name = NULL; switch (compression&CBF_COMPRESSION_MASK) { case CBF_CANONICAL: errorcode = cbf_compress_canonical (source, elsize, elsign, nelem, compression, file, &size, bits, realarray, byteorder, dimfast, dimmid, dimslow, padding); break; case CBF_PACKED: case CBF_PACKED_V2: case 0: errorcode = cbf_compress_packed (source, elsize, elsign, nelem, compression, file, &size, bits, realarray, byteorder, dimfast, dimmid, dimslow, padding); break; case CBF_BYTE_OFFSET: errorcode = cbf_compress_byte_offset (source, elsize, elsign, nelem, compression, file, &size, bits, realarray, byteorder, dimfast, dimmid, dimslow, padding); break; case CBF_NIBBLE_OFFSET: errorcode = cbf_compress_nibble_offset (source, elsize, elsign, nelem, compression, file, &size, bits, realarray, byteorder, dimfast, dimmid, dimslow, padding); break; case CBF_PREDICTOR: errorcode = cbf_compress_predictor (source, elsize, elsign, nelem, compression, file, &size, bits, realarray, byteorder, dimfast, dimmid, dimslow, padding); break; case CBF_H5COMPRESSION_ZLIB: if (!compression_name) compression_name = "HDF5 zlib"; case CBF_H5COMPRESSION_LZ4: if (!compression_name) compression_name = "HDF5 LZ4"; case CBF_H5COMPRESSION_LZ4_2: if (!compression_name) compression_name = "HDF5 LZ4**2"; CBF_PRINT_WARNING2(compression_name," not implemented in CBF files yet, treated as 'none'"); case CBF_NONE: errorcode = cbf_compress_none (source, elsize, elsign, nelem, compression, file, &size, bits, realarray, byteorder, dimfast, dimmid, dimslow, padding); break; default: errorcode = CBF_ARGUMENT; } /* Add the compressed size */ if (compressedsize) *compressedsize += size; /* Flush the buffers */ errorcode |= cbf_flush_bits (file); /* Get the digest? */ if (digest) errorcode |= cbf_end_digest (file, digest); /* Done */ return errorcode; } /* Get the parameters of an array (read up to the start of the table) */ int cbf_decompress_parameters (int *eltype, size_t *elsize, int *elsigned, int *elunsigned, size_t *nelem, int *minelem, int *maxelem, unsigned int compression, cbf_file *file) { unsigned int nelem_file; int errorcode, minelement_file, maxelement_file, elsigned_file, elunsigned_file; /* Discard any bits in the buffers */ file->bits [0] = 0; file->bits [1] = 0; /* Check compression type */ if (compression != CBF_CANONICAL && (compression&CBF_COMPRESSION_MASK) != CBF_PACKED && (compression&CBF_COMPRESSION_MASK) != CBF_PACKED_V2 && compression != CBF_BYTE_OFFSET && compression != CBF_NIBBLE_OFFSET && compression != CBF_PREDICTOR && compression != CBF_NONE) return CBF_FORMAT; if (compression == CBF_NONE || compression == CBF_BYTE_OFFSET || compression == CBF_NIBBLE_OFFSET) { nelem_file = 0; minelement_file = maxelement_file = 0; } else { /* Read the number of elements (64 bits) */ cbf_failnez (cbf_get_integer (file, (int *) &nelem_file, 0, 64)) /* Read the minimum element (64 bits) */ errorcode = cbf_get_integer (file, &minelement_file, 1, 64); if (errorcode && errorcode != CBF_OVERFLOW) return errorcode; /* Read the maximum element (64 bits) */ errorcode = cbf_get_integer (file, &maxelement_file, 1, 64); if (errorcode && errorcode != CBF_OVERFLOW) return errorcode; } /* Update the element sign, type, minimum, maximum and number */ elsigned_file = !(((unsigned) minelement_file) <= ((unsigned) maxelement_file) && ((signed) minelement_file) > ((signed) maxelement_file)); elunsigned_file = !(((signed) minelement_file) <= ((signed) maxelement_file) && ((unsigned) minelement_file) > ((unsigned) maxelement_file)); if (elsigned) *elsigned = elsigned_file; if (elunsigned) *elunsigned = elunsigned_file; if (eltype) *eltype = CBF_INTEGER; if (elsize) { /* Calculate the minimum number of bytes needed to hold the elements */ if (minelement_file == 0 && maxelement_file == 0) { *elsize = 0; } else { if ((!elsigned_file || ((signed) minelement_file == (signed short) minelement_file && (signed) maxelement_file == (signed short) maxelement_file)) || (!elunsigned_file || ((unsigned) minelement_file == (unsigned short) minelement_file && (unsigned) maxelement_file == (unsigned short) maxelement_file))) { if ((!elsigned_file || ((signed) minelement_file == (signed char) minelement_file && (signed) maxelement_file == (signed char) maxelement_file)) || (!elunsigned_file || ((unsigned) minelement_file == (unsigned char) minelement_file && (unsigned) maxelement_file == (unsigned char) maxelement_file))) { *elsize = sizeof (char); } else { *elsize = sizeof (short); } } else { *elsize = sizeof (int); } } } if (minelem) *minelem = minelement_file; if (maxelem) *maxelem = maxelement_file; if (nelem) *nelem = nelem_file; /* Success */ return 0; } /* Decompress an array (from the start of the table) */ int cbf_decompress (void *destination, size_t elsize, int elsign, size_t nelem, size_t *nelem_read, size_t compressedsize, unsigned int compression, int bits, int sign, cbf_file *file, int realarray, const char *byteorder, size_t dimover, size_t dimfast, size_t dimmid, size_t dimslow, size_t padding) { switch (compression&CBF_COMPRESSION_MASK) { case CBF_CANONICAL: return cbf_decompress_canonical (destination, elsize, elsign, nelem, nelem_read, compressedsize, compression, bits, sign, file, realarray, byteorder, dimover, dimfast, dimmid, dimslow, padding); case CBF_PACKED: case CBF_PACKED_V2: case 0: return cbf_decompress_packed (destination, elsize, elsign, nelem, nelem_read, compressedsize, compression, bits, sign, file, realarray, byteorder, dimover, dimfast, dimmid, dimslow, padding); case CBF_BYTE_OFFSET: return cbf_decompress_byte_offset (destination, elsize, elsign, nelem, nelem_read, compressedsize, compression, bits, sign, file, realarray, byteorder, dimover, dimfast, dimmid, dimslow, padding); case CBF_NIBBLE_OFFSET: return cbf_decompress_nibble_offset (destination, elsize, elsign, nelem, nelem_read, compressedsize, compression, bits, sign, file, realarray, byteorder, dimover, dimfast, dimmid, dimslow, padding); case CBF_PREDICTOR: return cbf_decompress_predictor (destination, elsize, elsign, nelem, nelem_read, compressedsize, compression, bits, sign, file, realarray, byteorder, dimover, dimfast, dimmid, dimslow, padding); case CBF_NONE: return cbf_decompress_none (destination, elsize, elsign, nelem, nelem_read, compressedsize, compression, bits, sign, file, realarray, byteorder, dimover, dimfast, dimmid, dimslow, padding); } /* Fail */ return CBF_ARGUMENT; } #ifdef __cplusplus } #endif